Table S1 - Host and Viral Genetic Correlates of Clinical Definitions of HIV-1 Disease Progression

Host genetic and viral results. For SNPs, 1 indicates the most common and 2 the variant allele. CCR5 haplotypes are presented according to published nomenclature, where CCR5 P1 is included in HHE, HHG*1 and HHF*1 (HHG*2 and HHF*2 were not considered as they include the protective alleles CCR5 Delta 32 and CCR2 V64I). Observed protective HLA alleles included B*2705, B*5701, B*5101, B*1302, A10 serogroup (A*2501, A*2601) and A*3201. Risk HLA alleles included B*35Px (B*3503), B22 serogroup (B*55, B*56), B*1801, A*2402 and A*2301. Participants are classified in the different classes according to the log of median viral load (Log VL), except for rapid progressors. For this class, individuals were ordered decrescendo according to time from seroconversion to CD4 <350. For elite controllers, the occasional blip was not considered for estimation of median Log VL. * non-B subtype viruses do not allow viral dating and X4/R5 genotyping. Score: simple additive genetic score that includes the most valuable genetic markers as explained in Materials and Methods. Quantification of DNA viral load, estimated by limiting dilution PCRs, was expressed as number of copies per million PBMCs. + charge: number of positive charged amino acids in the V3 loop. Ancest: Ancestral; Cauc: Caucasian; N.D.: not done; N.A.: not available. Mode HIV = mode of HIV acquisition; MSM: men having sex with men, HET: heterosexual, IDU: intravenous drug use. Green: protective factors; red: risk factors.
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